[gmx-users] Add additional LJ to certain atom pair- experience and a funny result

Mark Abraham mark.j.abraham at gmail.com
Fri Feb 21 23:34:42 CET 2014

If you want a reproducible trajectory, you should consider the thoughts
here http://www.gromacs.org/Documentation/Terminology/Reproducibility


On Fri, Feb 21, 2014 at 6:23 PM, jia jia <jzg579 at gmail.com> wrote:

> Dear all:
>    I'm trying to add additional LJ potential to certain atom pair, e.g. for
> atom 1 and 2, except normal atom LJ and Coulomb depend on atom type, I want
> add an additional LJ to them (so, only for atom 1 and 2, they will have
> Vorin+Vadd). I'm using gromcas 4.0.5 (double precision).
>    My way to do this is add a line for " 1 2 1 C6value C12value" to the
> paires as the gromacs does no scale 1-4 potential.
>    To test whether it work, I've set a system contain only two non-bonded
> atom, then perform two 1-cpu, 40 step simulation (output v, f every step),
> one simulation is with origin LJ potential, one simulation is add the line
> " 1 2 1 C6value C12value" to paires, and change the C6 C12 value of atom 1
> 2 in XXnb.itp (or other nonbond parameter file) to "0 0".
>    With this change, I'm expecting the two simulation give identical
> result.
>    I've checked the result with gmxdump, when using G53a6, yes, after 40
> step two siimulations give identical results.
>    However, when use Martini, the 0 - 10 step is identical, after that
> there is growing difference between them. At the end of 40steps, the
> difference in coordinations is about 0.0002 nm, and for the force is also
> about 0.0002.
>    If I run a simulation from a second time, the result from second run is
> indentical with  previous run. This suggest the differences are not from
> machine  error.
>    Has any one test this before or have any idea where this error from?
>    I doubt the error may from define variable, e.g. the progrom treat LJ
> and 1-4 interaction in different precision.
>    I'll contine test and check source, If I find anything I'll report here.
> Cheers
> Guang
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